Armour is one of the more important technological improvements you can start researching after first contact with the aliens. Even the first technological breakthrough in this area makes your aquanauts much more likely to survive a direct hit on the battlefield, and decreases the amount of time they'll spend recovering from wounds. It will help you build your agents experience much faster, and make the Battlescape somewhat more forgiving of mistakes and bad luck.
Diving Suit - Armored diving gear allowing X-COM agents to perform underwater operations at any depth.
Plastic Aqua Armor - New diving gear incorporating Aqua Plastics for greater defensive abilities.
Ion Armor - Heavy plates with Zrbite-powered muscle assist and air-filtering system.
Magnetic Ion Armor - Ion Armor with Magnetic Navigation system.
Armor Quick Comparison
|Plastic Aqua Armor*||60||35||35||30||25|
|Magnetic Ion Armor**||142||80||80||110||65|
* Grants 10% resistance to Armor Piercing, and 20% resistance to Gauss and Fire/Phosphor damage.
** Protects the wearer against all Fire/Phosphor damage, and grants 30% resistance to Gauss damage, 20% resistance to Armor Piercing and High Explosive damage, and 10% resistance to Sonic damage.
Just like your aquanauts, when one wearing armour dies, the armour's gone for good. So the only way to keep from losing armour is to keep your troopers alive.
In addition, if you're unhappy with the performance of your aquanauts and decide to have them sacked, be sure to remove the armour before doing so. If you do not then the disgruntled aquanaut will take the suit home with them and you will not see it again.
Finally, note that you will not get a chance to equip armour when a base defence mission is initiated. Therefore, be sure to equip your aquanauts with the armour you want before any alien sub assaults your base, or they will enter combat only wearing their diving suits.